SMTL ID : 6gbn.1 (1 other biounit)

Crystal structure of S-adenosyl-L-homocysteine hydrolase from Cytophaga hutchinsonii in complex with adenosine

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.09 Å

Oligo State

homo-tetramer

Ligands

4 x ADN: ADENOSINE(Non-covalent)

ADN.1: 19 residues within 4Å: Chain A: L.58, H.59, T.61, Q.63, T.64, D.137, E.162, T.163, K.192, D.196, H.307, L.350, L.353, T.357, G.358, H.359, M.364, F.368 Ligands: NAD.2 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:Q.63, A:E.162, A:T.163, A:K.192, A:K.192, A:H.307, A:H.359 ADN.5: 20 residues within 4Å: Chain B: L.58, H.59, T.61, Q.63, T.64, D.137, E.162, T.163, K.192, D.196, H.307, L.350, L.353, T.357, G.358, H.359, M.364, F.368 Ligands: NAD.6, NA.7 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:T.61, B:Q.63, B:T.64, B:T.163, B:T.163, B:K.192, B:K.192, B:H.307, B:H.359 ADN.9: 19 residues within 4Å: Chain C: L.58, H.59, T.61, Q.63, T.64, D.137, E.162, T.163, K.192, D.196, H.307, L.350, L.353, T.357, G.358, H.359, M.364, F.368 Ligands: NAD.10 7 PLIP interactions: 7 interactions with chain C Hydrogen bonds: C:Q.63, C:E.162, C:T.163, C:K.192, C:K.192, C:H.307, C:H.359 ADN.13: 20 residues within 4Å: Chain D: L.58, H.59, T.61, Q.63, T.64, D.137, E.162, T.163, K.192, D.196, H.307, L.350, L.353, T.357, G.358, H.359, M.364, F.368 Ligands: NAD.14, NA.15 9 PLIP interactions: 9 interactions with chain D Hydrogen bonds: D:T.61, D:Q.63, D:T.64, D:T.163, D:T.163, D:K.192, D:K.192, D:H.307, D:H.359

4 x NAD: NICOTINAMIDE-ADENINE-DINUCLEOTIDE(Non-covalent)

NAD.2: 30 residues within 4Å: Chain A: T.163, T.164, T.165, D.196, N.197, G.226, G.228, D.229, V.230, T.248, E.249, I.250, D.251, C.254, A.281, T.282, G.283, N.284, I.287, I.305, G.306, H.307, L.350, N.352, H.359 Chain B: L.415, Q.419, K.432, Y.436 Ligands: ADN.1 25 PLIP interactions: 19 interactions with chain A, 6 interactions with chain B Hydrophobic interactions: A:N.197, A:V.230 Hydrogen bonds: A:T.164, A:T.165, A:T.165, A:N.197, A:G.228, A:D.229, A:V.230, A:I.250, A:D.251, A:N.284, A:H.307, A:N.352, A:N.352, B:Q.419, B:K.432, B:K.432, B:Y.436, B:Y.436 Water bridges: A:G.231, A:T.248, A:G.283, A:F.308, B:Q.419 NAD.6: 29 residues within 4Å: Chain A: Q.419, K.432, Y.436 Chain B: T.163, T.164, T.165, D.196, N.197, G.226, G.228, D.229, V.230, T.248, E.249, I.250, D.251, C.254, A.281, T.282, G.283, N.284, I.287, I.305, G.306, H.307, L.350, N.352, H.359 Ligands: ADN.5 26 PLIP interactions: 21 interactions with chain B, 5 interactions with chain A Hydrophobic interactions: B:N.197, B:V.230 Hydrogen bonds: B:T.164, B:T.164, B:T.165, B:T.165, B:T.165, B:N.197, B:G.228, B:D.229, B:V.230, B:T.248, B:I.250, B:D.251, B:N.284, B:H.307, B:N.352, B:N.352, A:Q.419, A:K.432, A:K.432 Water bridges: B:T.165, B:G.231, B:F.308, A:D.413, A:Q.419 NAD.10: 30 residues within 4Å: Chain C: T.163, T.164, T.165, D.196, N.197, G.226, G.228, D.229, V.230, T.248, E.249, I.250, D.251, C.254, A.281, T.282, G.283, N.284, I.287, I.305, G.306, H.307, L.350, N.352, H.359 Chain D: L.415, Q.419, K.432, Y.436 Ligands: ADN.9 25 PLIP interactions: 6 interactions with chain D, 19 interactions with chain C Hydrogen bonds: D:Q.419, D:K.432, D:K.432, D:Y.436, D:Y.436, C:T.164, C:T.165, C:T.165, C:N.197, C:G.228, C:D.229, C:V.230, C:I.250, C:D.251, C:N.284, C:H.307, C:N.352, C:N.352 Water bridges: D:Q.419, C:G.231, C:T.248, C:G.283, C:F.308 Hydrophobic interactions: C:N.197, C:V.230 NAD.14: 29 residues within 4Å: Chain C: Q.419, K.432, Y.436 Chain D: T.163, T.164, T.165, D.196, N.197, G.226, G.228, D.229, V.230, T.248, E.249, I.250, D.251, C.254, A.281, T.282, G.283, N.284, I.287, I.305, G.306, H.307, L.350, N.352, H.359 Ligands: ADN.13 26 PLIP interactions: 21 interactions with chain D, 5 interactions with chain C Hydrophobic interactions: D:N.197, D:V.230 Hydrogen bonds: D:T.164, D:T.164, D:T.165, D:T.165, D:T.165, D:N.197, D:G.228, D:D.229, D:V.230, D:T.248, D:I.250, D:D.251, D:N.284, D:H.307, D:N.352, D:N.352, C:Q.419, C:K.432, C:K.432 Water bridges: D:T.165, D:G.231, D:F.308, C:D.413, C:Q.419

4 x NA: SODIUM ION(Non-functional Binders)

NA.3: 4 residues within 4Å: Chain A: Q.63, T.357, G.358, H.359 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain C Hydrogen bonds: A:Q.63, A:G.358 Water bridges: A:T.357, C:D.214 NA.7: 6 residues within 4Å: Chain B: Q.63, T.357, G.358, H.359, P.360 Ligands: ADN.5 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Q.63, B:T.357 Water bridges: B:Q.63 NA.11: 4 residues within 4Å: Chain C: Q.63, T.357, G.358, H.359 4 PLIP interactions: 1 interactions with chain A, 3 interactions with chain C Water bridges: A:D.214, C:T.357 Hydrogen bonds: C:Q.63, C:T.357 NA.15: 6 residues within 4Å: Chain D: Q.63, T.357, G.358, H.359, P.360 Ligands: ADN.13 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:T.357, D:G.358 Water bridges: D:Q.63

2 x PG4: TETRAETHYLENE GLYCOL(Non-functional Binders)

PG4.4: 5 residues within 4Å: Chain A: K.384, Y.385, K.388, V.389, Y.390 No protein-ligand interaction detected (PLIP) PG4.12: 5 residues within 4Å: Chain C: K.384, Y.385, K.388, V.389, Y.390 No protein-ligand interaction detected (PLIP)

2 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.8: 2 residues within 4Å: Chain B: R.402, D.428 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.402 Water bridges: B:R.402, B:R.402 PEG.16: 2 residues within 4Å: Chain D: R.402, D.428 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:R.402 Water bridges: D:R.402, D:R.402

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Czyrko, J. et al., Crystal structure of S-adenosyl-L-homocysteine hydrolase from Cytophaga hutchinsonii, a case of combination of crystallographic and non-crystallographic symmetry. Croatica Chemica Acta (2018)

Release Date

2018-08-08

Peptides

Adenosylhomocysteinase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

Adenosylhomocysteinase

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